InspiredResearch Winter 2013 Issue 4 Research News from the Department of Computer Science, University of Oxford CITIES OF SLIME Computational Biology Group models bacteria to boost understanding of biofilm – p4 Facebook Photos: The Hidden message Student’s tool for hiding secret messages in Facebook photos hits headlines – p16 Nature flies in with a solution Distributed computing problem solved by studying how flies’ cells develop – p8 Chips with confidence Collaboration between Oxford and Intel to improve chips – p6 InSpired NEWS Research… Oxford sweeps up Prominent Paper is a twice-yearly newsletter published by the Department BCS accolades Award for artificial of Computer Science at Oxford University. intelligence research If you would like to learn more Thomas Lukasiewicz and his co- about anything you read in these Dr Boris Motik authors have won the prestigious pages please get in touch: AIJ Prominent Paper Award 2013 for Department of Computer Science, the paper ‘Combining answer set University of Oxford, Samson Abramsky FRS Prof. programming with description logics Wolfson Building, for the Semantic Web’. Parks Road, Oxford, OX1 3QD Two academics from Oxford’s This paper proposes dl-programs, a [email protected] Computer Science Department have been recognised by BCS, The formalism that integrates description Chartered Institute for IT, for their logics with rule-based logic programs outstanding contribution to the field. under answer set semantics. It Editorial board provides not only detailed theoretical Suzanna Marsh (editor) Dr Boris Motik has been named as the recipient of the BCS Roger analyses of these programs in Helen Wilcox (freelance editor) terms of their expressive power and Suvarna Designs (designer) Needham Award while Professor Samson Abramsky FRS has received computational complexities, but also Wendy Adams the BCS Lovelace Medal. an implementation that illustrates the Bob Coecke usefulness of the proposed formalism Ivan Flechais Their prizes include the opportunity in the Semantic Web. Jeremy Gibbons to deliver a public lecture about Leslie Ann Goldberg their research. Dr Motik will present This work highlights many difficult Fred Hoffman the 2013 BCS Needham lecture in issues in the problem of adding rules Shoshannah Holdom November, and Professor Abramsky and default rules into description Alexander Horn will deliver the Lovelace lecture in 2014. logics, and has been very influential in Peter Jeavons subsequent work in this area. Thomas Lukasiewicz Boris, whose work has had an impact Kelly Ryan both inside and outside academia, Professorship links Maureen York has made major contributions to the design and standardisation of the industry and academia OWL2 ontology language, which is The Royal Society has for the Contributors widely used in industrial research and first time awarded a Research Samson Abramsky applications. His research is around Professorship to an industry scientist, Phil Armstrong the development of techniques for which will enable him to embark on Nycole Cain intelligent management of large academic research while retaining Jassim Happa amounts of data. his position in industry. The award Sophie Kay has been made to Dr Luca Cardelli, Elias Koutsoupias Samson is pre-eminent in setting the a top computer scientist at Microsoft Marta Kwiatkowska modern agenda in the foundations Research, to take up an honorary Sharon Lloyd of computer science, an area where position at Oxford’s Department of Thomas Lukasiewicz he has made immense contributions Computer Science. Ines Marusic since the 1980s. His contributions in Peter Millican each of the past three decades had He will use his professorship to Gary Mirams a major impact on the field, notably: work at the interface of biology, Boris Motik Domain Theory in Logical Form, nanotechnology and computing, as Blanca Rodriguez Game Semantics and Categorical he believes that the convergence of Kelly Ryan Quantum Mechanics. His work over these scientific disciplines will bring William Smith the past decade has shown that about the greatest future changes methods and concepts developed in healthcare and technology. He in theoretical computer science can has strong interests in investigating be applied very directly in quantum computational structures in biology Printed on recycled paper information, and the foundations of and in engineering computational quantum mechanics itself. structures from biologic materials. 2 InSpired Research: Research news from the Department of Computer Science, University of Oxford NEWS Fellowships galore new foundations for quantum logic. the Northeast of the United States The prize is awarded once every two no longer occur. Stefan joined the Oxford computer scientists have years during the award ceremony Department of Computer Science as received a lot of recognition for held at the bi-annual conference a postdoctoral research assistant in their research over the past few of the International Quantum November 2009. months, receiving fellowships from Structures Association. the EPSRC, the Royal Society, Stanislav has returned to take up a the ERC and the Wellcome Trust, Phil was awarded the EPSRC post at Oxford this October where he plus an Honorary Fellowship from fellowship for his project entitled will work on his project ‘Optimisation ESCMSET, and the Birkhoff – von ‘Bayesian Models of Grammar of separable functions’. He obtained Neumann prize. Induction and Translation’. His his Doctor of Philosophy in Computer research programme aims to Science at Oxford in 2009. Since Dr Chris Heunen and Dr Phil develop large-scale and language- then he has worked for Microsoft Blunsom have been successful in independent algorithms to allow Research Cambridge, the University gaining highly sought after five- for syntactic analyses of real world of Oxford, and was most recently at year EPSRC Fellowships. Chris of language data, without the need the University of Warwick when he the Quantum Group has received for traditional hand annotation. The applied for the Fellowship. funding for his project ‘Combining development of such a model could Viewpoints in Quantum Theory’, increase our understanding of how Dr Blanca Rodriguez has been which intends to use computer children learn languages and could awarded a five-year Wellcome science, physics and mathematics to lead to the development of advanced Trust Senior Research Fellowship in progress our understanding of and language technologies for processing Biomedicial Sciences, and Dr Gary capabilities in quantum computing. online data. Mirams the five-year Henry Dale These advancements could greatly Fellowship, which will support their ease the future development of Additionally, prestigious Royal Society work in the field of Computational protocols for quantum hardware. University Research Fellowships have Medicine. See p13 for more details of Chris has held a Junior Research been awarded to Dr Stefan Kiefer and Blanca and Gary’s work. Fellowship since joining the Dr Stanislav Živný, which will fund Department in 2010. their research for the next five years. Professor Kevin Burrage has been awarded an Honorary Fellowship Chris has also been awarded the Stefan’s project ‘Quantitative Analysis by the European Society of 2012 Birkhoff – von Neumann prize of Infinite-State Systems’ centres on Computational Methods in Sciences, for his research, which includes computer-aided formal verification Engineering and Technology the analysis of quantum logic from to ensure that dynamic, infinite state (ESCMSET), its highest distinction, the perspective of categorical logic systems behave as they are intended. for his outstanding contribution in the and the study of how algebraic Improved computer-aided verification fields of Computational Mathematics quantum mechanics can be related could, in future, ensure that incidents and Numerical Analysis. to topos theory so as to construct such as the 2003 power blackout in ERC Professor Leslie Ann Goldberg of computational counting has been awarded a five-year problems, determining which advanced European Research Council problems are tractable, and which Advanced Grant for her project are intractable; and to discover grant ‘Mapping the Complexity of complexity characterisations awarded Counting’, to start in March which elucidate the features that 2014. The overall objectives make counting problems tractable are: to map out the landscape or intractable. NEWS FLASH £1.26 Million Platform Grant for Information Systems The Information Systems Group has just been awarded a highly sought after Platform Grant from EPSRC. Platform Grants provide a base of flexible funding to support the retention of key staff, feasibility studies, longer term research and international networking. Congratulations to all involved in making this application a success. We will bring you details of the research in future editions. www.cs.ox.ac.uk Issue 4, Winter 2013 3 Cities of slime Most bacteria live together in quasi-social colonies, which are known for exhibiting fascinating behaviour. The way that these biofilms grow is currently being modelled by The Oxford Computational Biology Group. In this article, Will Smith explains why slimy layers of bacteria are so important, and describes some of the group’s current research. What do you imagine when you hear computational modelling. For Recent work performed in the the word ‘bacteria’? Perhaps some example, biofilms can form intricate Computational Biology Group little green blobs swimming about, structures during growth;